Genetically Sequencing Healthy Babies Yielded Surprising Results
Today in Melrose, Massachusetts, Cora Stetson is the picture of good health, a bubbly precocious 2-year-old. But Cora has two separate mutations in the gene that produces a critical enzyme called biotinidase and her body produces only 40 percent of the normal levels of that enzyme.
In the last few years, the dream of predicting and preventing diseases through genomics, starting in childhood, is finally within reach.
That's enough to pass conventional newborn (heelstick) screening, but may not be enough for normal brain development, putting baby Cora at risk for seizures and cognitive impairment. But thanks to an experimental study in which Cora's DNA was sequenced after birth, this condition was discovered and she is being treated with a safe and inexpensive vitamin supplement.
Stories like these are beginning to emerge from the BabySeq Project, the first clinical trial in the world to systematically sequence healthy newborn infants. This trial was led by my research group with funding from the National Institutes of Health. While still controversial, it is pointing the way to a future in which adults, or even newborns, can receive comprehensive genetic analysis in order to determine their risk of future disease and enable opportunities to prevent them.
Some believe that medicine is still not ready for genomic population screening, but others feel it is long overdue. After all, the sequencing of the Human Genome Project was completed in 2003, and with this milestone, it became feasible to sequence and interpret the genome of any human being. The costs have come down dramatically since then; an entire human genome can now be sequenced for about $800, although the costs of bioinformatic and medical interpretation can add another $200 to $2000 more, depending upon the number of genes interrogated and the sophistication of the interpretive effort.
Two-year-old Cora Stetson, whose DNA sequencing after birth identified a potentially dangerous genetic mutation in time for her to receive preventive treatment.
(Photo courtesy of Robert Green)
The ability to sequence the human genome yielded extraordinary benefits in scientific discovery, disease diagnosis, and targeted cancer treatment. But the ability of genomes to detect health risks in advance, to actually predict the medical future of an individual, has been mired in controversy and slow to manifest. In particular, the oft-cited vision that healthy infants could be genetically tested at birth in order to predict and prevent the diseases they would encounter, has proven to be far tougher to implement than anyone anticipated.
But in the last few years, the dream of predicting and preventing diseases through genomics, starting in childhood, is finally within reach. Why did it take so long? And what remains to be done?
Great Expectations
Part of the problem was the unrealistic expectations that had been building for years in advance of the genomic science itself. For example, the 1997 film Gattaca portrayed a near future in which the lifetime risk of disease was readily predicted the moment an infant is born. In the fanfare that accompanied the completion of the Human Genome Project, the notion of predicting and preventing future disease in an individual became a powerful meme that was used to inspire investment and public support for genomic research long before the tools were in place to make it happen.
Another part of the problem was the success of state-mandated newborn screening programs that began in the 1960's with biochemical tests of the "heel-stick" for babies with metabolic disorders. These programs have worked beautifully, costing only a few dollars per baby and saving thousands of infants from death and severe cognitive impairment. It seemed only logical that a new technology like genome sequencing would add power and promise to such programs. But instead of embracing the notion of newborn sequencing, newborn screening laboratories have thus far rejected the entire idea as too expensive, too ambiguous, and too threatening to the comfortable constituency that they had built within the public health framework.
"What can you find when you look as deeply as possible into the medical genomes of healthy individuals?"
Creating the Evidence Base for Preventive Genomics
Despite a number of obstacles, there are researchers who are exploring how to achieve the original vision of genomic testing as a tool for disease prediction and prevention. For example, in our NIH-funded MedSeq Project, we were the first to ask the question: "What can you find when you look as deeply as possible into the medical genomes of healthy individuals?"
Most people do not understand that genetic information comes in four separate categories: 1) dominant mutations putting the individual at risk for rare conditions like familial forms of heart disease or cancer, (2) recessive mutations putting the individual's children at risk for rare conditions like cystic fibrosis or PKU, (3) variants across the genome that can be tallied to construct polygenic risk scores for common conditions like heart disease or type 2 diabetes, and (4) variants that can influence drug metabolism or predict drug side effects such as the muscle pain that occasionally occurs with statin use.
The technological and analytical challenges of our study were formidable, because we decided to systematically interrogate over 5000 disease-associated genes and report results in all four categories of genetic information directly to the primary care physicians for each of our volunteers. We enrolled 200 adults and found that everyone who was sequenced had medically relevant polygenic and pharmacogenomic results, over 90 percent carried recessive mutations that could have been important to reproduction, and an extraordinary 14.5 percent carried dominant mutations for rare genetic conditions.
A few years later we launched the BabySeq Project. In this study, we restricted the number of genes to include only those with child/adolescent onset that could benefit medically from early warning, and even so, we found 9.4 percent carried dominant mutations for rare conditions.
At first, our interpretation around the high proportion of apparently healthy individuals with dominant mutations for rare genetic conditions was simple – that these conditions had lower "penetrance" than anticipated; in other words, only a small proportion of those who carried the dominant mutation would get the disease. If this interpretation were to hold, then genetic risk information might be far less useful than we had hoped.
Suddenly the information available in the genome of even an apparently healthy individual is looking more robust, and the prospect of preventive genomics is looking feasible.
But then we circled back with each adult or infant in order to examine and test them for any possible features of the rare disease in question. When we did this, we were surprised to see that in over a quarter of those carrying such mutations, there were already subtle signs of the disease in question that had not even been suspected! Now our interpretation was different. We now believe that genetic risk may be responsible for subclinical disease in a much higher proportion of people than has ever been suspected!
Meanwhile, colleagues of ours have been demonstrating that detailed analysis of polygenic risk scores can identify individuals at high risk for common conditions like heart disease. So adding up the medically relevant results in any given genome, we start to see that you can learn your risks for a rare monogenic condition, a common polygenic condition, a bad effect from a drug you might take in the future, or for having a child with a devastating recessive condition. Suddenly the information available in the genome of even an apparently healthy individual is looking more robust, and the prospect of preventive genomics is looking feasible.
Preventive Genomics Arrives in Clinical Medicine
There is still considerable evidence to gather before we can recommend genomic screening for the entire population. For example, it is important to make sure that families who learn about such risks do not suffer harms or waste resources from excessive medical attention. And many doctors don't yet have guidance on how to use such information with their patients. But our research is convincing many people that preventive genomics is coming and that it will save lives.
In fact, we recently launched a Preventive Genomics Clinic at Brigham and Women's Hospital where information-seeking adults can obtain predictive genomic testing with the highest quality interpretation and medical context, and be coached over time in light of their disease risks toward a healthier outcome. Insurance doesn't yet cover such testing, so patients must pay out of pocket for now, but they can choose from a menu of genetic screening tests, all of which are more comprehensive than consumer-facing products. Genetic counseling is available but optional. So far, this service is for adults only, but sequencing for children will surely follow soon.
As the costs of sequencing and other Omics technologies continue to decline, we will see both responsible and irresponsible marketing of genetic testing, and we will need to guard against unscientific claims. But at the same time, we must be far more imaginative and fast moving in mainstream medicine than we have been to date in order to claim the emerging benefits of preventive genomics where it is now clear that suffering can be averted, and lives can be saved. The future has arrived if we are bold enough to grasp it.
Funding and Disclosures:
Dr. Green's research is supported by the National Institutes of Health, the Department of Defense and through donations to The Franca Sozzani Fund for Preventive Genomics. Dr. Green receives compensation for advising the following companies: AIA, Applied Therapeutics, Helix, Ohana, OptraHealth, Prudential, Verily and Veritas; and is co-founder and advisor to Genome Medical, Inc, a technology and services company providing genetics expertise to patients, providers, employers and care systems.
Diagnosed by App: Medical Testing in the Palm of Your Hand
Urinary tract infections aren't life-threatening, but they can be excruciatingly painful and debilitating.
"Overnight, I'd be gripped by this searing pain and I can barely walk," says Ling Koh, a Los Angeles-based bioengineer. But short of going to the ER or urgent care, she'd have to suffer for a few days until she could get in to see her family doctor for an antibiotic prescription.
Smartphones are now able to do on-the-spot diagnostic tests that were previously only able to be performed in a lab.
No longer. Koh, who works for Scanwell Health, was instrumental in the development of the company's smartphone app that is FDA-cleared for urinary tract infection screening. It allows someone to test urine at home using a paper test strip — the same one used by doctors in ERs and labs. The phone app reads a scan card from the test kit that can analyze what's on the strip and then connect the patient to a physician who can make a virtual diagnosis.
Test strips cost $15 for a three-pack and consultation with a doc is about the same as an average co-pay -- $25, and the app matches the quality of clinical laboratory tests, according to the company. Right now, you can get a referral to a telehealth visit with a doctor in California and get a prescription. A national rollout is in the works within the next couple of months.
"It's so easy to use them at home and eliminate the inefficiencies in the process," says Koh. "A telemedicine doctor can look at the test results and prescribe directly to the pharmacy instead of women waiting at home, miserable, and crying in the bathtub."
Scanwell is now involved in an ongoing National Institutes of Health- sponsored study of chronic kidney disease to test a version of the app to identify patients who have the disease, which affects more than 30 million Americans. "Because kidney disease has virtually no symptoms, by the time people realize they're sick, their illness is advanced and they're ready for dialysis," says Koh. "If we can catch it sooner, early intervention can help them avoid kidney failure."
Smartphones have changed society — and now they may change medical care, too. Thanks to the incredible processing capabilities of our smartphones, which come equipped with a camera, access to the internet and are thousands of times faster than the 1960s era NASA computers that ran the Apollo Moon Mission, these pocket-sized powerhouses have become an invaluable tool for managing our health and are even able to do on-the-spot diagnostic tests that were previously only able to be performed in a lab.
This shift to in-home testing is the wave of the future, promising to ease some of the medical care bottlenecks in which patients can have two- to three-week waits to see their family doctors and lift some of the burdens on overworked physicians.
"This is really the democratization of medicine because a lot of the things we used to rely on doctors, hospitals, or labs to do we'll be able to do ourselves," says Dr. Eric Topol, an eminent cardiologist and digital health pioneer at the Scripps Clinic and Research Institute in La Jolla.
But troubling questions remain. Aside from the obvious convenience, are these tests truly as accurate as ones in a doctor's office? And with all this medical information stored and collected by smartphones, will privacy be sacrificed? Will friends, family members, and employers suddenly have access to personal medical information we'd rather keep to ourselves?
The range of what these DIY health care apps can do is mind-boggling, and even more complex tests are on the way.
"I'm really worried about that because we've let our guard down," says Topol. "Data stored on servers is a target for cyber thieves — and data is being breached, hacked, brokered, and sold, and we're complacent."
Still, the apps have come a long way since 2011 when Topol whipped out an experimental smartphone electro-cardiogram that he had been testing on his patients when a fellow passenger on a flight from Washington D.C. was seized with severe chest pains. At 35,000 feet in the air, the app, which uses fingertip sensors to detect heart rate, showed the man was having a heart attack. After an emergency landing, the passenger was rushed to the closest hospital and survived. These days, even the Apple Watch has an FDA-approved app that can monitor your electro-cardiogram readings.
The range of what these DIY health care apps can do is mind-boggling, and even more complex tests are on the way. Phone apps can now monitor sleep quality to detect sleep apnea, blood pressure, weight and temperature. In the future, rapid diagnostic tests for infectious diseases, like flu, Dengue or Zika, and urinalysis will become common.
"There is virtually no limit to the kinds of testing that can be done using a smartphone," says Dr. John Halamka, Executive Director of the Health Technology Exploration Center at Beth Israel Lahey Health. "No one wants to drive to a clinician's office or lab if that same quality testing can be achieved at a lower cost without leaving home."
SkinVision's skin cancer screening tool, for instance, can tell if a suspicious mole is cancerous. Users take three photos, which are then run through the app's algorithm that compares their lesions with more than three million pictures, evaluating such elements as asymmetry, color, and shape, and spits out an assessment within thirty seconds. A team of in-house experts provide a review regardless of whether the mole is high or low risk, and the app encourages users to see their doctors. The Dutch-based company's app has been used by more than a million people globally in the EU, and in New Zealand and Australia, where skin cancer is rampant and early detection can save lives. The company has plans to enter the U.S. market, according to a spokesperson.
Apps like Instant Heart Rate analyze blood flow, which can indicate whether your heart is functioning normally, while uChek examines urine samples for up to 10 markers for conditions like diabetes and urinary tract infections. Some behavioral apps even have sensors that can spot suicide risks if users are less active, indicating they may be suffering from a bout of the blues.
Even more complex tests are in the research pipeline. Apps like ResAppDX could eventually replace x-rays, CT scans, and blood tests in diagnosing severe respiratory infections in kids, while an EU-funded project called i-Prognosis can track a variety of clues — voice changes, facial expressions, hand steadiness — that indicate the onset of Parkinson's disease.
These hand-held testing devices can be especially helpful in developing countries, and there are pilot programs to use smartphone technology to diagnose malaria and HIV infections in remote outposts in Africa.
"In a lot of these places, there's no infrastructure but everyone has a smartphone," says Scanwell's Koh. "We need to leverage the smartphone in a clinically relevant way."
However, patient privacy is an ongoing concern. A 2019 review in the Journal of the American Medical Association conducted by Australian and American researchers looked at three dozen behavioral health apps, mainly for depression and smoking cessation. They found that about 70 percent shared data with third parties, like Facebook and Google, but only one third of them disclosed this in a privacy policy.
"Patients just blindly accept the end user agreements without understanding the implications."
Users need to be vigilant, too. "Patients just blindly accept the end user agreements without understanding the implications," says Hamalka, who is also the Chief Information Officer and Dean for Technology at Harvard Medical School.
And quality control is an issue. Right now, the diagnostic tools currently available have been vetted by the FDA, and overseas companies like Skin Vision have been scrutinized by the U.K.'s National Health Service and the EU. But the danger is that a lot of apps are going to be popping up soon that haven't been properly tested, due to loopholes in the regulations.
"All we want," says Topol, "are rigorous studies to make sure what consumers are using is validated."
[Correction, August 19th, 2019: An earlier version of this story misstated the specifics of SkinVision's service. A team of in-house experts reviews users' submissions, not in-house dermatologists, and the service is not free.]
Last year, we sponsored a short story contest, asking writers to share a fictional vision of how emerging technology might shape the future. This year, the competition has a new spin.
The Prompt:
Write a personal essay of up to 2000 words describing how a new advance in medicine or science has profoundly affected your life.
The Rules:
Submissions must be received by midnight EST on September 20th, 2019. Send your original, previously unpublished essay as a double-spaced attachment in size 12 Times New Roman font to kira@leapsmag.com. Include your name and a short bio. It is free to enter, and authors retain all ownership of their work. Upon submitting an entry, the author agrees to grant leapsmag one-time nonexclusive publication rights.
All submissions will be judged by the Editor-in-Chief on the basis of insightfulness, quality of writing, and relevance to the prompt. The Contest is open to anyone around the world of any age, except for the friends and family of leapsmag staff and associates.
The winners will be announced by October 31st, 2019.
The Prizes:
Grand Prize: $500, publication of your story on leapsmag, and promotion on our social media channels.
First Runner-Up: $100 and a shout-out on our social media channels.
Good luck!
Kira Peikoff was the editor-in-chief of Leaps.org from 2017 to 2021. As a journalist, her work has appeared in The New York Times, Newsweek, Nautilus, Popular Mechanics, The New York Academy of Sciences, and other outlets. She is also the author of four suspense novels that explore controversial issues arising from scientific innovation: Living Proof, No Time to Die, Die Again Tomorrow, and Mother Knows Best. Peikoff holds a B.A. in Journalism from New York University and an M.S. in Bioethics from Columbia University. She lives in New Jersey with her husband and two young sons. Follow her on Twitter @KiraPeikoff.